Delimiting species and quantifying their underlying variation is imperative for documenting diversity in highly speciose regions like the Neotropics. To aid with proper delimitation and avoid the perils of inflating or underestimating taxonomic units, approaches combining environmental, genetic, and phenotypic data are essential to provide a holistic perspective based on integrative taxonomy. A multiple-evidence approach is particularly useful when dealing with cryptic or iconic (i.e., easy to identify) species that might contain hidden diversity. We studied the phylogeography of one such species, the frog-eating bat (Trachops), and examined species limits throughout its broad range in the Neotropics. Following previous studies, we tested the hypotheses that Trachops is a monotypic genus with high intraspecific genetic and phenotypic diversity. Multilocus phylogenetics and species-delimitation analyses showed that Trachops consists of at least three species that diverged between seven to three million years ago. Taxonomic limits of three species-level groups recognized in our study (T. cirrhosus, T. coffini, and T. ehrhardti) are confirmed by a cranial morphometric analysis of over 800 individuals and craniodental features. Ecological niche models revealed that each of these groups occupies a distinct niche, and heterogeneous environmental gradients and biogeographic barriers could be responsible for maintaining the limits of these taxa. This study sheds new light into the taxonomy of Trachops that can be important for conservation management in Neotropical areas with a fast rate of deforestation.